Pickle the red onions - pack the red onions in a large mason jar. Pour the water, vinegar and salt on top and shake. Press onions down so they are all submerged. If it needs more liquid, just add equal parts water and vinegar. Let it sit overnight or for at least 1 hour.
Cook quinoa if you don’t have it prepped. Add quinoa to a medium pet along with 1 ½ cups water. Bring to a boil, then simmer, covered, for 15 minutes or until the water has evaporated and quinoa grains have burst open. Remove from heat and let sit, covered, for 5 minutes. Fluff with a fork and set aside.
Add all ingredients for the beans to a medium bowl and toss to coat. Set aside.
In a large pot or dutch oven over medium heat, add the olive oil and tomato paste. Cook the tomato paste, stirring occasionally, for 3 minutes or until it darkens in color and starts sticking to the pot. Stir in the fennel seeds and red pepper flakes and cook for 30 seconds.
Add in the sliced chard stems and ½ teaspoon salt and cook for 1 minute, stirring often, or until softened. Add in half of the chard (tearing the leaves into pieces while adding to the pot), garlic (if using), and remaining ¼ teaspoon salt and cook, stirring frequently, until the chard has wilted down, about 1 minute. Add the remaining chard and cook, stirring frequently, lifting the bottom cooked chard/stems to the top, until it has all wilted down, about 5 minutes. Continue to cook until most of the water has evaporated and a thicker tomato sauce starts to form, about 2 minutes more. Stir in the lemon juice.
Serve quinoa with the chard and beans and top with a drizzle of the bean marinade and pickled onions.